[2024-01-24 14:06:30,733] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:30,735] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:30,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f544728-946a-4058-85bd-ff3c3cf19202/dqc_reference
[2024-01-24 14:06:32,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:32,084] [INFO] Task started: Prodigal
[2024-01-24 14:06:32,085] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf257c58-f8b5-45e3-b49f-dae15ae07350/GCF_004342175.1_ASM434217v1_genomic.fna.gz | prodigal -d GCF_004342175.1_ASM434217v1_genomic.fna/cds.fna -a GCF_004342175.1_ASM434217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:44,309] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:44,310] [INFO] Task started: HMMsearch
[2024-01-24 14:06:44,310] [INFO] Running command: hmmsearch --tblout GCF_004342175.1_ASM434217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f544728-946a-4058-85bd-ff3c3cf19202/dqc_reference/reference_markers.hmm GCF_004342175.1_ASM434217v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:44,637] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:44,639] [INFO] Found 6/6 markers.
[2024-01-24 14:06:44,685] [INFO] Query marker FASTA was written to GCF_004342175.1_ASM434217v1_genomic.fna/markers.fasta
[2024-01-24 14:06:44,686] [INFO] Task started: Blastn
[2024-01-24 14:06:44,686] [INFO] Running command: blastn -query GCF_004342175.1_ASM434217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f544728-946a-4058-85bd-ff3c3cf19202/dqc_reference/reference_markers.fasta -out GCF_004342175.1_ASM434217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:45,568] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:45,571] [INFO] Selected 17 target genomes.
[2024-01-24 14:06:45,572] [INFO] Target genome list was writen to GCF_004342175.1_ASM434217v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:45,604] [INFO] Task started: fastANI
[2024-01-24 14:06:45,604] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf257c58-f8b5-45e3-b49f-dae15ae07350/GCF_004342175.1_ASM434217v1_genomic.fna.gz --refList GCF_004342175.1_ASM434217v1_genomic.fna/target_genomes.txt --output GCF_004342175.1_ASM434217v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:01,146] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:01,146] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f544728-946a-4058-85bd-ff3c3cf19202/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:01,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f544728-946a-4058-85bd-ff3c3cf19202/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:01,160] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:07:01,160] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:07:01,160] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	80.9788	730	1348	95	below_threshold
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	80.6904	679	1348	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	80.6322	555	1348	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	80.4623	593	1348	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	80.4039	601	1348	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	80.2605	656	1348	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	78.9601	431	1348	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	78.5483	450	1348	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	78.4431	414	1348	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	78.3443	466	1348	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	78.2219	387	1348	95	below_threshold
Allochromatium warmingii	strain=DSM 173	GCA_900107145.1	61595	61595	type	True	77.5729	205	1348	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	77.4196	279	1348	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.5295	159	1348	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.1389	126	1348	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.1015	128	1348	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.9935	113	1348	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:01,162] [INFO] DFAST Taxonomy check result was written to GCF_004342175.1_ASM434217v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:01,163] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:01,163] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:01,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f544728-946a-4058-85bd-ff3c3cf19202/dqc_reference/checkm_data
[2024-01-24 14:07:01,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:01,209] [INFO] Task started: CheckM
[2024-01-24 14:07:01,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342175.1_ASM434217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342175.1_ASM434217v1_genomic.fna/checkm_input GCF_004342175.1_ASM434217v1_genomic.fna/checkm_result
[2024-01-24 14:07:40,360] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:40,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:40,381] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:40,381] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:40,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342175.1_ASM434217v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:40,382] [INFO] Task started: Blastn
[2024-01-24 14:07:40,383] [INFO] Running command: blastn -query GCF_004342175.1_ASM434217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f544728-946a-4058-85bd-ff3c3cf19202/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342175.1_ASM434217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:41,640] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:41,644] [INFO] Selected 14 target genomes.
[2024-01-24 14:07:41,644] [INFO] Target genome list was writen to GCF_004342175.1_ASM434217v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:41,679] [INFO] Task started: fastANI
[2024-01-24 14:07:41,679] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf257c58-f8b5-45e3-b49f-dae15ae07350/GCF_004342175.1_ASM434217v1_genomic.fna.gz --refList GCF_004342175.1_ASM434217v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342175.1_ASM434217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:56,160] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:56,177] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:56,178] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_004342175.1	s__Thiobaca trueperi	100.0	1347	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiobaca	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000227745.2	s__Chromatium violascens	81.0023	726	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653465.1	s__Chromatium minus	80.6705	681	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018409545.1	s__Allochromatium tepidum	80.6255	556	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903866365.1	s__Chromatium sp903866365	80.5429	672	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	80.4654	593	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCF_013385175.1	s__Allochromatium humboldtianum	80.3813	601	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583575.1	s__Thiocystis violacea	80.2396	658	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720725.1	s__Allochromatium palmeri	79.9335	575	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585215.1	s__Imhoffiella purpurea	79.5861	591	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224065.1	s__Imhoffiella drewsii	79.2858	536	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012276755.1	s__Marichromatium bheemlicum	78.4528	413	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390875.1	s__Thiocapsa sp011390875	78.1099	354	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107145.1	s__Allochromatium warmingii	77.545	207	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:56,179] [INFO] GTDB search result was written to GCF_004342175.1_ASM434217v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:56,180] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:56,184] [INFO] DFAST_QC result json was written to GCF_004342175.1_ASM434217v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:56,184] [INFO] DFAST_QC completed!
[2024-01-24 14:07:56,184] [INFO] Total running time: 0h1m25s